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Yorodumi- PDB-5w0v: Crystal structure of full-length Kluyveromyces lactis Kap123 with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w0v | ||||||
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Title | Crystal structure of full-length Kluyveromyces lactis Kap123 with histone H4 1-34 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Budding yeast karyopherin / 23 HEAT repeats with a right-handed superhelical solenoid structure / Histone NLS recognition / The extra-long helix of the repeat 23 | ||||||
Function / homology | Function and homology information HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / replication fork protection complex / Oxidative Stress Induced Senescence ...HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / replication fork protection complex / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / nuclear localization sequence binding / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / small GTPase binding / protein import into nucleus / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Kluyveromyces lactis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.821 Å | ||||||
Authors | An, S. / Yoon, J. / Song, J.-J. / Cho, U.-S. | ||||||
Citation | Journal: Elife / Year: 2017 Title: Structure-based nuclear import mechanism of histones H3 and H4 mediated by Kap123. Authors: An, S. / Yoon, J. / Kim, H. / Song, J.J. / Cho, U.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w0v.cif.gz | 793.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w0v.ent.gz | 659.2 KB | Display | PDB format |
PDBx/mmJSON format | 5w0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/5w0v ftp://data.pdbj.org/pub/pdb/validation_reports/w0/5w0v | HTTPS FTP |
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-Related structure data
Related structure data | 5vchSC 5ve8C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 122968.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (yeast) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CMF0 #2: Protein/peptide | Mass: 3537.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Kluyveromyces lactis (yeast) / References: UniProt: P02309*PLUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.76 % / Description: brick-shaped crystals |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate (pH 6.5), 0.2M sodium acetate, 30% PEG 4000 and 5% Jeffamin M-600 |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.821→50 Å / Num. obs: 59828 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.045 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.821→2.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 5938 / Rpim(I) all: 0.479 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VCH Resolution: 2.821→33.787 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.821→33.787 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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